Tuesday, August 25, 2009

A new international research facility is due to be built at the DESY site, Hamburg, Germany: an X-ray Free Electron Laser (XFEL). The promise is that lasing will be possible at such short wavelength that structural biology can be done with single copies of biomolecules, membranes, cells ... So it should open access to high-resolution structures of biological entities that cannot be crystallised.

Monday, August 24, 2009

Saw the mexican movie Sin Nombre this weekend, and loved it to bits. Am still all stirred and shaken.

There are many good things about it, but if I may add a scientific point to the reviews that are already out there -- it is intriguing how the two main character are driven by economic inequality along intersecting gradients. One migrating along the wealth gradient from Honduras to the US, the other driven into organised crime by the inequality within the Mexican society. As their trajectories intersect and they meet as strangers on a train (very literally), and the dramatic story unfolds from there ...

It's very depressing to reflect on the social realities that have shaped these lives -- the film doesn't discuss the issues at all, only shows their dreadful impact on people, but I think that is a good thing as it allows viewers to think for themselves.

So catch it while you can.

PS Also, I understand that this is the first movie co-produced by the company Canana, set up by mexican actors Diego Luna and Gael Garcia Bernal. Very promising debut.

Sunday, August 23, 2009

"I pushed through rush-choked channels scarcely wider than my boat. I found backwaters no one had navigated for years. I stumbled across cannabis gardens and camouflaged shelters where fugitives lived. ... Abandoned behind railway fences, on the edge of playing fields, anonymously skirting business units, I found places I had never imagined possible, a parallel world."

I have made very similar discoveries in the last 3 years, it's quite amazing how a city can turn its back to its rivers. Apart from the main punting highway, it really is a parallel Oxford that one gets to see from the waterways.

Unlike GM, however, I don't trouble the fish (the rest of the article in Saturday's Guardian is about fishing). I only watch the wildlife (and have seen a kingfisher too!)

Here's a recent photo of our family canoe, taken upstream at the sunnymeade recreation ground.

Saturday, August 22, 2009

I really like the paper on Raman spectroscopy of ancient art works, out in PNAS this week.

First of all, what a cool job, being in the "department of scientific research" of the Metropolitan Museum of Art at New York, scraping tiny little bits off great paintings and analysing where the artists bought their colours :)

But seriously, I think this modified Raman method the author has optimised for the application to artworks looks promising, as it allows to identify organic pigments with only a microscopically small sample, which was previously nearly impossible.

While his previous efforts on detecting dyes in solution or in fabric fibres were published in the Journal of Raman Spectroscopy, what got this one into PNAS was obviously the fact that the author not only managed to adapt the technique to paintings and glazes on sculptures, but that he also pushed back the record for the earliest records of humans preparing organic dyes from plants or animals by a cool 7 centuries by studying 4000 year old sample from the Middle Kingdom.

Thursday, August 20, 2009

Climbing up the Montmartre hill in search of Amélie vistas, all we could actually see was people photographing each other. I wonder how they made the movie, did they have the area cleared by force beforehand ?

Never mind Sacré Coeur, the main attraction at the top was a guy doing tricks with a football while standing on a plinth over the steep descent towards central Paris:

which is of course compelling to watch mainly because you realise that if he drops the ball, he may have to run all the way down to Place Pigalle to get it back. He never did drop it though.

On the way down we saw Picasso's first atelier in Paris, but I haven't got a picture of that. Finishing off by the riverside where we started, here is a view of the beautiful backside of Notre Dame, as seen from upstream:

Wednesday, August 19, 2009

An article in last week's technology section of the Guardian claims Wikipedia approaches its limits and suggests that Wikipedia will stop growing because the "deletionists" won the war against the "inclusionists".

However, if you think about how an encyclopedia starting from scratch at time zero is likely to grow (given a huge and growing pool of enthusiastic contributors), it is obvious that there will be a very steep increase in the number of entries initially, as it has to "catch up" with the knowledge that was there before it started. Once all that (or at least the vaguely relevant parts of it) are included, it can slow down and only grow at the rate at which new knowledge is produced (e.g. in the scientific literature, and by current affairs). which is still significant growth rate (and probably exponential as well), but slower than the catching up phase.

So the observed slowdown is perfectly reasonable. Don't know what wars are going on behind the scenes at Wikipedia, but from the growth trend alone, there's no need to conclude that there are any.

Tuesday, August 18, 2009

If anybody wants a tourist-free attraction in Paris, or just a nice spot to relax, I recommend the Canal St. Martin, which runs just northeast of the Gare de l'Est, and mysteriously disappears below ground before it joins the Seine.

On a short stretch of canal, it has an implausible amount of 19th century technology, including high footbridges, locks, and a rotating bridge.

Between Gare de l'Est and the canal there is also a very nice park (whose name I forgot), and in the park-side front of the office building next to the park I spotted this slightly unusual biotope during my stopover in June (en route to Germany):

But by the time I returned to the spot last week, the tree had disappeared and the lifeless order of things had been restored. Also along the canal, this somewhat expressionistic architectural detail:

While the Oxford piece is open access, the C&I one is premium content, I'm afraid. So you'd need to be a member of the SCI or have institutional access of some kind. Or find a hardcopy in your library. Or be very nice to me.

Abstract is free, though: They may be investigating topics as diverse as bird migration or quantum information processing, protein structure and hydrogen storage materials, but what links the research of nearly a dozen groups across the science departments at the University of Oxford is electron spin resonance (ESR) spectroscopy. Until recently, this technique was the domain of a small circle of chemists specialising on electron spin, but the advent of user-friendly instrumentation and of interdisciplinary research centres has broadened the user base considerably.

Friday, August 14, 2009

I have just come back from a 3 nights trip to Paris which was quite fantastic. Thanks to my son who has autism and is addicted to walking, I've probably seen more of the city than on my previous visits put together.

We were based at a small hotel near the Porte St. Martin, less than 1km north of the centre Pompidou (Beaubourg) arts centre, which looks like this:

It was regarded as outrageously hyper-modern in the 70s, but I think it has aged quite well and now that time has caught up a bit, it makes a nice landmark, and it has become my main focus point and "living room" when I'm in Paris. during a visit in 2002, I bought a xaphoon (a small instrument that sounds a lot like a saxophone if you can play it well, which I can't) on the square outside the centre, and I was pleased to see that the xaphoon vendor was still there (or maybe a colleague, didn't remember his face).

Walking past the Beaubourg we get to the north bank of the Seine, of course, where the city beach has become a yearly tradition by now, and to the Pont Neuf

which is the costar of a classic movie with Juliette Binoche, Les Amants du Pont Neuf. The film is set during a renovation of the bridge ahead of the 1989 bicentenary of the French revolution, but wasn't finished by the time the bridge reopened, so they had to build a mock bridge somewhere in the south and ended up with the most expensive French movie ever.

Further down, the Pont des arts, a pedestrian bridge which was a new discovery for me (I only knew it from the chanson by Brassens: Si par hasard, 'sus le pont des arts, tu croise le vent ... ). I found out that from this bridge one has the most stunning view ever, of the Ile de la cite upstream, and the Eiffel tower downstream, not to mention the various buildings on the banks facing the bridge.

we also did a guided river cruise, down to the Eiffel tower and back, and learned lots of things from that (I usually avoid such touristy activities, but the things we do for the kids ... )

Away from the Seine, we also explored the Canal St. Martin and Montmartre, about which I'll post separately.

According to plans drawn up by the DESERTEC consortium, most of Europe's energy needs could be supplied from large scale solar power plants in North Africa and the Middle East. The plan is based on concentrating solar-thermal power plants and a high-voltage direct current (HVDC) grid. It has recently come a step closer to realisation with the signing of an agreement between a dozen major companies, launching the Desertec Industrial Initiative.

Saturday, August 08, 2009

Apparently, the UK government is now also backing major investment in high-speed railway lines for the UK. The Tories have already called for such plans as an alternative to the insane expansion of Heathrow airport planned by Labour.

Celebrating the occasion, the Guardian has run a series of features on high speed railways in other countries. The piece about France is here, and in the margin, under "More on this story", you'll find links to reports from other countries. (also see my recent comments on the French TGVs

As for the UK investment in high speed tracks, I'll believe that when I see it, but let's at least applaud the good intentions now proclaimed by both major parties.

Friday, August 07, 2009

Natural receptors and newly developed biosensors such as aptamer sensors share the key feature that they undergo structural change during binding of a ligand.

Kevin Plaxco and co-workers at Santa Barbara have now shown in a PNAS paper released this week that a simple thermodynamic model involving only three states can explain the response of such receptors or sensors. The states involved are (1) nonbinding state, (2) binding competent state, and then (3) ligand-bound state, with a "switch" equilibrium constant governing the change from (1) to (2) and a binding constant the move from (2) to (3).

From the group's press blurb:

In their PNAS paper, Alexis Vallée-Bélisle of UCSB, collaborator Francesco Ricci of the University of Rome Tor Vergata, and senior author Prof. Kevin Plaxco, describe and test a simple mathematical “population-shift” model that will allow biotech researchers to fine-tune the ease with which artificial biomolecular switches can be “flipped”. It also sheds light on how natural biomolecular switches evolved.

Specifically, they show that switching reflects a fundamental trade-off. On the one hand, in the absence of the input signal, the “off” state of the switch must be more stable than its “on” state in order to allow more switches to occupy the “off” state where they are poised to respond to the target and generate a large output signal. On the other hand, if the “off” state is too stable the switch will require much more input signal before it will flip. Optimal switch performance –optimal sensitivity to the switching agent- is thus achieved when the off state is neither too stable nor too unstable. Vallée-Bélisle’s population-shift model describes the relationship between off-state stability and switch sensitivity, thus providing researchers an approach to rationally optimize the performance of artificial switches, and providing insights into the evolution of their naturally occurring analogs.

Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors

Alexis Vallée-Bélisle, Francesco Riccia, and Kevin W. Plaxco

Published online before print August 5, 2009, doi: 10.1073/pnas.0904005106

Thursday, August 06, 2009

I have now read the paper on the 40,000 year old flute from the Hohle Fels cave in Southwest Germany, which came out in print in today's issue of Nature (online in June). Really exciting stuff. Just imagine you're going through a layer of sediment which you know with absolute certainty to be > 35 k years old and you find bits of a musical instrument. The first author says in the front section of the magazine that it was a shock, which is probably an understatement. I would probably have died from a heart attack on the spot.

Looking at the photos, the instrument looks really sophisticated as well. For instance, the surroundings of the holes are flattened to make it easier to find the hole and to close it precisely with the finger. The mouthpiece looks intriguing as well. In the interview at the front of the magazine the first author says that a replica of the flute is now available (finding a matching vulture bone seems to have been the rate-limiting step!), so I am looking forward to finding out more about the musical properties of the instrument.

Also, still intrigued about a possible link with the vaguely simultaneous disappearance of the Neanderthals (about which there is a nice feature by Kate Wong in the August issue of Scientific American). The image of a pied piper comes to mind ...

Tuesday, August 04, 2009

Two weeks into the Twitter experience I need to sum up before I forget what life was like before twitter ...

I have to admit that I only joined a bit reluctantly, but it all turned out a lot better than I expected.

For instance, the asymmetric "following" tool, as opposed to the mutually agreed "friendship" on MySpace. I was kind of expecting this to produce a class society where celebreties broadcast what they had for breakfast and followers just follow. I was surprised to find that in practice it is a lot more democratic than that, as most people "follow back" as a matter of courtesy, and even celebrities occasionally answer to the tweets of common people.

I really like the power of the simple linking between people using the @username tool -- that must be the easiest networking tool ever invented. Also the automatic recognition and abbreviation of hyperlinks is a clever trick.

140 characters is a limit I can live with -- which in fact often requires the use of some creativity to fit the message in, so it's a bit like poetry. If I do have something much longer to say, I put it on the blog and post a summary with a link on twitter.

As a way of making new contacts, it turns out to be much more efficient than MySpace or FaceBook -- I have gained as many followers in 2 weeks as I have FaceBook friends after 2 years.

Finally, it is really intriguing to see how fast the Twitterverse is evolving its own specific culture, with new language (tweets, tweeps, twibes ...) and new traditions (e.g. #followfriday). Social scientists should scrap whatever they were doing before and just point all their telescopes at the twitterverse.

What I'm missing is the music and the detailed profile pages from MySpace. In a perfect social networking world, I would have MySpace as the platform with twitter replacing the messages, comments and bulletins. MySpace missed a trick here.